Meet the principal investigators
Zaida Luthey-Schulten is director of the NSF Science and Technology Center for Quantitative Cell Biology. Martin Gruebele is the associate director.
Job title Director
Zaida "Zan" Luthey-Schulten isprimarily responsible for the GPU-based integrative cell modeling of 4D whole cell models (4DWCMs) and knowledge transfer with NVIDIA. She is responsible for all NSF reporting requirements.
She received a B.S. in Chemistry from the University of Southern California in 1969, a M.S. in Chemistry from Harvard University in 1972, and a Ph.D. in Applied Mathematics from Harvard University in 1975. From 1975 to 1980, she was a Research Fellow at the Max-Planck Institute for Biophysical Chemistry in Goettingen, and from 1980 to 1985, a Research Fellow in the Department of Theoretical Physics at the Technical University of Munich. She is theMurchison-Mallory Endowed Chair in Chemistry. Zan closely collaborates with many theory and experimental groups in the center, as well as outside groups, to unify -omics, microscopy and many other types of data into 4DWCMs of bacterial, yeast and human cells.
Job title Associate Director
Martin is responsible for imaging and tracking experimental efforts with MINFLUX and will coordinate with the computational and outreach teams, as well as the director and team leaders. He and Glenn Fried are the primary contact for knowledge transfer with Abberior Instruments.
He received his B.S. in 1984, and his Ph.D. in 1988, both from the UC Berkeley. After working as a postdoctoral fellow at Caltech, he joined the faculty of the University of Illinois in 1992. He is theJames R. Eiszner Endowed Chair in Chemistry. His group studies virus capsids and beads ranging in size from 30-150 nm in live cells, using MINFLUX as a probe of mesoscale structure in nucleus and cytoplasm via diffusion, and will measure interactions between individual pairs of proteins in the live mammalian cell using MINFLUX, including spliceosome and other dynamic organelles where the whole-cell models need inputs. Published collaborations with Zan Luthey-Schulten, Emad Tajkorshid and others in the center focus on whole-cell and even organismal dynamics.
Rohit Bhargava View Rohit Bhargava in Beckman directory
Rohit is a team leader for advanced optical experiments, such as IR tomography and optogenetics. His lab is engaged in fundamental advances in measurement technology that can record spectroscopic data from exceptionally small volumes of single cells. Rohit and his colleagues advanced previous methods to increase greatly the reliability and speed of chemical imaging data. They are currently working with Mark Anastasio to develop more sensitive spectral analysis methods with signal processing of recorded data. They are working with Martin Gruebele to quantify spectral properties of metabolites. And, they have started working with Angad Mehta group to chemically image changes in yeast mitochondrial dynamics alter metabolism. Rohit also directs the Cancer Center at Illinois, with synergies in imaging and how cells respond to perturbations.
Sharlene is responsible for overseeing the Broader Impacts aims of the STC for Quantitative Cell Biology. She serves on the Executive Committee and chairs the Inclusion, Diversity, Equity, and Access (IDEA) committee. She will manage outreach, diversity, and professional development programs for the center, including the annual Summer School in Quantitative Cell Biology, the Villa-Cisse Scholars Program, the Summer Sabbatical, and STC-QCB CARES Program.
She received her B.S. in Biochemistry and Molecular Biology from the UC Santa Cruz and her Ph.D. in Biophysics and Quantitative Biology from Illinois. She is currently a Teaching Assistant Professor in the Physics Department at UIUC, where she oversees the development of courses in biological physics to be ported to other universities with help of the QCB, as well as many diversity and public engagement initiatives.
Unit title European Molecular Biology Laboratory
Julia contributed to advancement of cryo-focused ion beam preparations from intact cells, their synergy with state-of-the-art cryo-electron microscopy imaging, spearheaded the development of 3D cryo-correlative confocal fluorescence microscopy for site-specific preparations, and pioneered cryo-FIB lift-out for visual proteomics in multicellular specimens. She and her group at the EMBL, an international team of interdisciplinary researchers, continue to develop cryo-electron tomography to achieved unprecedented resolution for macromolecular complexes and their organization inside cells to give rise to complex biology. They will collaborate with members of the STC to harness these data towards constructing realistic ultrastructural and molecular representations of whole cells.
Angad's team leads the chemical biology components of center research. His lab has created yeast mutants that alter mitochondrial function and could alter mitochondrial networks. He uses fluorescence confocal imaging to test the correlation between mitochondrial function or dysfunction genotypes to changes in the mitochondrial dynamics. His group collaborates with Rohit Bhargava’s lab to perform imaging studies to investigate how changes in yeast mitochondrial dynamics alter metabolism. Angad’s lab has generated transcriptomics data for the minimal cell (strain syn1), and is currently working with HPCBio and Zan Luthey-Schulten’s lab to analyze the transcriptional profile of the minimal cells. They are also working on generating more replicates of these transcriptomics datasets. This is expected to inform operons, operonic structure, and relative abundances of all the transcripts within the minimal cell. They have also worked with Taekjip Ha’s lab on imaging studies of the minimal cell to study its cell division process.
Emad Tajkhorshid View Emad Tajkhorshid in Beckman directory
Emad is the team leader for the atomistic simulation efforts and their interface with whole cell models. His research group develops and applies molecular modeling, simulation, and visualization to the investigation of dynamics-function relationships in biomolecular systems and processes. Major themes include investigation of membrane protein function, studying functional lipid-protein interactions at a microscopic level, and characterization of other membrane-associated phenomena. The group recently moved into the challenging area of cell-scale modeling and simulation, focusing mostly on membrane assemblies, such as the viral envelopes and capsids. A recent key collaboration between Emad and Martin focused on the stability of the capsid in Hepatitis B virus. A key aspect to success has been close collaboration with leading experimental groups.
He has authored more than 300 peer-reviewed articles addressing complex mechanistic aspects of biomolecular systems and processes using a variety of established and novel computational techniques. He is Director of the NIH Resource Center for Macromolecular Modeling and Visualization, the creator of VMD and NAMD, in which STC faculty members Luthey-Schulten and Aksimentiev are directly involved as well, with a long-standing mission to establish efficient and accessible modeling, visualization, and simulation technologies for the biomedical community with strong user support.
Aleksei and his group are developing multi-resolution computational approaches to unravel physical principles that govern essential biological processes. In collaboration with the center’s experimentalists, they investigate how proteins and RNA diffuse through the cytoplasm, and how nuclear transport is enabled by the nuclear pore complex.
Mark and his team develop and validate novel computational methods for image analysis that will leverage MINFLUX and other data to advance the scientific mission of the center. They will also develop image formation methods that will enhance the capabilities of chemical imaging using infrared spectra, in collaboration with Bhargava and Zhang.
Mikael and his group will explore the theoretical and experimental limits of MINFLUX for biological microscopy tasks beyond single-particle localization, including orientation-dependent single particle imaging in live cells.
Stephen Boppart View Stephen Boppart in Beckman directory
Stephen and his Biophotonics Imaging Laboratory team use novel label-free multi-modal nonlinear imaging methods to investigate mitochondrial and other organelle dynamics and distributions in living cells to understand the effect of stress on cells under varying metabolic states and stressors, working with Zhang and Bhargava to metabolite dynamics.
Glenn Fried and his colleagues at the IGB Core will be managing the MINFLUX microscope as well as adding AI tools for volume EM imaging and sequential FISH labeling. Glenn is also a main center contact with industry partner Abberior.
Unit title J. Craig Venter Institute
John and his JCVI team are experts in the culture, genetic manipulation, and biochemical analysis of the minimal bacterial cell they constructed, JCVI-syn3A. They will provide other QCB teams advice about working with those bacteria and as needed and will build and analyze minimal cell mutants to assist other QCB teams.
Ido and his lab illuminate the spatiotemporal dynamics of fundamental processes in bacterial cells using MINFLUX, single-molecule tracking (collaboration with Sangjin Kim), STORM and PAINT (collaboration with Paul Selvin). Ido also works with the Mehta group to characterize the transcriptional activity of individual cyanobacterial cells as they colonize a yeast host, en route to establishing endosymbiosis.
William will provide high performance computing expertise, particularly for parallel performance of applications and I/O, as well as providing access to the Delta and Delta AI supercomputers at NCSA, and massive data storage modalities needed for sharing and disseminating center data.
Unit title Harvard Medical School
Taekjip’s team will use MINFLUX and multiplexed DNA-PAINT imaging in combination with genome-wide mapping of DNA mechanics and nucleosome condensation in collaboration with Prasanth and Aksimentiev to provide unique biophysical inputs to mesoscale modeling of chromosome organization and dynamics performed by Luthey-Schulten.
Unit title University of Texas Rio Grande Valley
Hyeonjun and his research team elucidate the underlying working mechanisms of DNA-binding proteins. They will enhance their research capabilities and provide critical data for whole cell models by utilizing MINFLUX to study how DNA-bound proteins behave on DNA under different experimental conditions.
Sangjin and her group will study the diffusion dynamics of macromolecules involved in gene expression in bacteria cells using MINFLUX, supporting one of the three cell types for which the center builds 4DWCMs.
Unit title University of Maryland, Baltimore County
Minjoung and her group will employ MINFLUX to investigate the internal structure of glucosomes, multienzyme condensates within human cells, across different cellular stress conditions and during the interactions with other cellular compartments.
Unit title Stockholm University and KTH Royal Institute of Technology
Erik’s team is developing molecular simulation technology in GROMACS to enable modeling, simulation and analysis of systems with hundreds of millions to billions of particles. They are also combining cryo-EM and cryo-ET data, such as collected by Mahamid’s group, with molecular modeling.
Unit title University of Groningen
Siewert-Jan and his group will perform coarse-grained simulations of cellsd to provide a dynamic cells at near-atomic resolution, to be linked with more coarse grained and whole cell models my machine-learning-based techniques.
Paola’s team will examine the dynamics of the bacterial chromosome at the initiation steps of chromosome replication and segregation using the MINFLUX system and collaborate with the Luthey-Schulten and Kim teams to model centromere segregation in bacteria.
Eric will coordinate science communication activities and research including facilitation of trainings and workshops for faculty and students associated with the center, offering a graduate level class in communicating science, and developing a formal certificate in science communication for the center that will provide opportunities for individuals beyond the university.
Kannanganattu V. Prasanth
Kannanganattu’s laboratory will use the MINFLUX microscope to quantify the dynamic interactions of nuclear domain-resident RNA binding proteins during various cellular stresses in eukaryotic cells, complementing investigations such as Gruebele’s MINFLUX-spliceosome studies.
Unit title Fisk University
Lei and his group will use machine learning techniques to study protein function in cells. He is also in charge of the program outreach effort for the center at Fisk University.
Luisa and the I-STEM evaluation team will monitor, document and report on the implementation, effectiveness, impact, and institutionalization of the STC-QCB’s research, outreach and educational activities and guide the Center via understanding and improvement of “program theory.”
Paul and his group will use the MINFLUX to detect fast “half-steps” of kinesin and dynein in three dimensions and as a function of force, as well as develop magnetic bead force measurements for MINFLUX.
Shuleiand his group are developing machine learning methods and advanced statistical computational tools for large and complex biological data sets, including multi-omics and imaging data, like MINFLUX, used by Gruebele, Backlund and others to maximize data extraction.
Yingjie and his group will develop a new infrared tomography system for 3-D chemical profiling of metabolites in live cells with sub-cellular resolution. This work is done in close collaboration with the Bhargava group among others.
- Kristopher Keipert, NVIDIA
- John Stone, NVIDIA
- Christian Wurm, Abberior Instruments
The University of Illinois Urbana-Champaign is partnering on this research with collaborators and colleagues from:
- Fisk University
- European Molecular Biology Lab
- Harvard Medical School
- J. Craig Venter Institute
- KTH Royal Institute of Technology
- Stockholm University
- University of Groningen
- University of Maryland, Baltimore County
- University of Texas Rio Grande Valley